documentation_config.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'\\nPurpose: To apply the documentation pipeline to package that will\\n\\n1) Clean module files (fix docstring, relative paths, ect)\\n2) Create the requirements file\\n3) Create the setup.py file\\n4) Verify pip install works\\n5) setup the sphinx documentation folders and push to github pages of repo\\n\\n\\n'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "\"\"\"\n",
    "Purpose: To apply the documentation pipeline to package that will\n",
    "\n",
    "1) Clean module files (fix docstring, relative paths, ect)\n",
    "2) Create the requirements file\n",
    "3) Create the setup.py file\n",
    "4) Verify pip install works\n",
    "5) setup the sphinx documentation folders and push to github pages of repo\n",
    "\n",
    "\n",
    "\"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'graph_tools'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "directory_name = \"graph_tools\"\n",
    "directory_name"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Cleaning current package"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/neurd_packages/graph_tools/graph_tools'"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from pathlib import Path\n",
    "directory = directory_name\n",
    "directory = str(Path(f\"./{directory}/\").absolute())\n",
    "directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "---- working on directory: /neurd_packages/graph_tools/graph_tools ---\n",
      "   --- working on module: /neurd_packages/graph_tools/graph_tools/epidemics_utils.py ---\n",
      "output_path = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "Search for package for /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "Matched to /neurd_packages/graph_tools/graph_tools/\n",
      "curr_mod = epidemics_utils, curr_package_name = graph_tools\n",
      "\n",
      "\n",
      "--- working on package: datasci_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "\n",
      "\n",
      "--- working on package: machine_learning_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "\n",
      "\n",
      "--- working on package: pytorch_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "\n",
      "\n",
      "--- working on package: graph_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 1\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "-- easier relative replacement --\n",
      "# of substitutions = 1\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "-- harder relative replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "\n",
      "\n",
      "--- working on package: meshAfterParty ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "\n",
      "\n",
      "--- working on package: neuron_morphology_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/epidemics_utils.py\n",
      "# of multi-line strings = 0\n",
      "# of matches (unique = True) = 3\n",
      "# of modules replaced = 3\n",
      "----non_pkg_mods_str = \n",
      "import matplotlib.pyplot as plt\n",
      "import numpy as np\n",
      "\n",
      "\n",
      "----pkg_mods_str = \n",
      "\n",
      "\n",
      "\n",
      "----own_mod_str = \n",
      "from . import epidemics_utils as epu\n",
      "   --- working on module: /neurd_packages/graph_tools/graph_tools/graph_path_utils.py ---\n",
      "output_path = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "Search for package for /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "Matched to /neurd_packages/graph_tools/graph_tools/\n",
      "curr_mod = graph_path_utils, curr_package_name = graph_tools\n",
      "\n",
      "\n",
      "--- working on package: datasci_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 2\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "\n",
      "\n",
      "--- working on package: machine_learning_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "\n",
      "\n",
      "--- working on package: pytorch_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "\n",
      "\n",
      "--- working on package: graph_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "-- easier relative replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "-- harder relative replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "\n",
      "\n",
      "--- working on package: meshAfterParty ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "\n",
      "\n",
      "--- working on package: neuron_morphology_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_path_utils.py\n",
      "# of multi-line strings = 0\n",
      "# of matches (unique = True) = 7\n",
      "# of modules replaced = 7\n",
      "----non_pkg_mods_str = \n",
      "import matplotlib.pyplot as plt\n",
      "import networkx as nx\n",
      "import numpy as np\n",
      "import time\n",
      "\n",
      "\n",
      "----pkg_mods_str = \n",
      "#--- from datasci_tools ---\n",
      "from datasci_tools import networkx_utils as xu\n",
      "from datasci_tools import tqdm_utils as tqdmu\n",
      "from datasci_tools.tqdm_utils import tqdm\n",
      "\n",
      "\n",
      "----own_mod_str = \n",
      "\n",
      "   --- working on module: /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py ---\n",
      "output_path = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "Search for package for /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "Matched to /neurd_packages/graph_tools/graph_tools/\n",
      "curr_mod = graph_preprocessing, curr_package_name = graph_tools\n",
      "\n",
      "\n",
      "--- working on package: datasci_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 2\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "\n",
      "\n",
      "--- working on package: machine_learning_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "\n",
      "\n",
      "--- working on package: pytorch_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "\n",
      "\n",
      "--- working on package: graph_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 1\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "-- easier relative replacement --\n",
      "# of substitutions = 1\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "-- harder relative replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "\n",
      "\n",
      "--- working on package: meshAfterParty ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "\n",
      "\n",
      "--- working on package: neuron_morphology_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_preprocessing.py\n",
      "# of multi-line strings = 0\n",
      "# of matches (unique = True) = 4\n",
      "# of modules replaced = 4\n",
      "----non_pkg_mods_str = \n",
      "import numpy as np\n",
      "\n",
      "\n",
      "----pkg_mods_str = \n",
      "#--- from datasci_tools ---\n",
      "from datasci_tools import networkx_utils as nx\n",
      "from datasci_tools import networkx_utils as xu\n",
      "\n",
      "\n",
      "----own_mod_str = \n",
      "from . import graph_preprocessing as gpre\n",
      "   --- working on module: /neurd_packages/graph_tools/graph_tools/graph_statistics.py ---\n",
      "output_path = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "Search for package for /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "Matched to /neurd_packages/graph_tools/graph_tools/\n",
      "curr_mod = graph_statistics, curr_package_name = graph_tools\n",
      "\n",
      "\n",
      "--- working on package: datasci_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 2\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "\n",
      "\n",
      "--- working on package: machine_learning_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "\n",
      "\n",
      "--- working on package: pytorch_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "\n",
      "\n",
      "--- working on package: graph_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 2\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "-- easier relative replacement --\n",
      "# of substitutions = 2\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-- harder relative replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "\n",
      "\n",
      "--- working on package: meshAfterParty ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "\n",
      "\n",
      "--- working on package: neuron_morphology_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_statistics.py\n",
      "# of multi-line strings = 1\n",
      "# of matches (unique = True) = 15\n",
      "# of modules replaced = 15\n",
      "----non_pkg_mods_str = \n",
      "from itertools import chain\n",
      "from networkx.algorithms import approximation as app\n",
      "from networkx.algorithms import distance_measures as dist\n",
      "from tqdm import tqdm\n",
      "import ndlib\n",
      "import ndlib.models.ModelConfig as mc\n",
      "import ndlib.models.epidemics as ep\n",
      "import networkx as nx\n",
      "import numpy as np\n",
      "import powerlaw\n",
      "import scipy\n",
      "import time\n",
      "\n",
      "\n",
      "----pkg_mods_str = \n",
      "#--- from graph_tools ---\n",
      "from . import graph_visualizations as gviz\n",
      "\n",
      "#--- from datasci_tools ---\n",
      "from datasci_tools import networkx_utils as xu\n",
      "\n",
      "\n",
      "----own_mod_str = \n",
      "from . import graph_statistics as gs\n",
      "   --- working on module: /neurd_packages/graph_tools/graph_tools/graph_visualizations.py ---\n",
      "output_path = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "Search for package for /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "Matched to /neurd_packages/graph_tools/graph_tools/\n",
      "curr_mod = graph_visualizations, curr_package_name = graph_tools\n",
      "\n",
      "\n",
      "--- working on package: datasci_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 4\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "\n",
      "\n",
      "--- working on package: machine_learning_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "\n",
      "\n",
      "--- working on package: pytorch_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "\n",
      "\n",
      "--- working on package: graph_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 2\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "-- easier relative replacement --\n",
      "# of substitutions = 2\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "-- harder relative replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "\n",
      "\n",
      "--- working on package: meshAfterParty ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "\n",
      "\n",
      "--- working on package: neuron_morphology_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/graph_visualizations.py\n",
      "# of multi-line strings = 1\n",
      "# of matches (unique = True) = 10\n",
      "# of modules replaced = 10\n",
      "----non_pkg_mods_str = \n",
      "import matplotlib\n",
      "import matplotlib.pyplot as plt\n",
      "import networkx as nx\n",
      "import numpy as np\n",
      "import pandas as pd\n",
      "\n",
      "\n",
      "----pkg_mods_str = \n",
      "#--- from graph_tools ---\n",
      "from . import graph_statistics as gs\n",
      "\n",
      "#--- from datasci_tools ---\n",
      "from datasci_tools import matplotlib_utils as mu\n",
      "from datasci_tools import numpy_utils as nu\n",
      "from datasci_tools import pandas_utils as pu\n",
      "\n",
      "\n",
      "----own_mod_str = \n",
      "from . import graph_visualizations as gviz\n",
      "   --- working on module: /neurd_packages/graph_tools/graph_tools/netsci_utils.py ---\n",
      "output_path = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "Search for package for /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "Matched to /neurd_packages/graph_tools/graph_tools/\n",
      "curr_mod = netsci_utils, curr_package_name = graph_tools\n",
      "\n",
      "\n",
      "--- working on package: datasci_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 2\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "\n",
      "\n",
      "--- working on package: machine_learning_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "\n",
      "\n",
      "--- working on package: pytorch_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "\n",
      "\n",
      "--- working on package: graph_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 1\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "-- easier relative replacement --\n",
      "# of substitutions = 1\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "-- harder relative replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "\n",
      "\n",
      "--- working on package: meshAfterParty ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "\n",
      "\n",
      "--- working on package: neuron_morphology_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/netsci_utils.py\n",
      "# of multi-line strings = 1\n",
      "# of matches (unique = True) = 7\n",
      "# of modules replaced = 7\n",
      "----non_pkg_mods_str = \n",
      "import matplotlib.pyplot as plt\n",
      "import netsci.metrics.motifs as nsm\n",
      "import netsci.visualization as nsv\n",
      "import numpy as np\n",
      "import seaborn as sns\n",
      "\n",
      "\n",
      "----pkg_mods_str = \n",
      "#--- from datasci_tools ---\n",
      "from datasci_tools import matplotlib_utils as mu\n",
      "\n",
      "\n",
      "----own_mod_str = \n",
      "from . import netsci_utils as nsu\n",
      "   --- working on module: /neurd_packages/graph_tools/graph_tools/null_models.py ---\n",
      "output_path = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "Search for package for /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "Matched to /neurd_packages/graph_tools/graph_tools/\n",
      "curr_mod = null_models, curr_package_name = graph_tools\n",
      "\n",
      "\n",
      "--- working on package: datasci_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "\n",
      "\n",
      "--- working on package: machine_learning_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "\n",
      "\n",
      "--- working on package: pytorch_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "\n",
      "\n",
      "--- working on package: graph_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "-- easier relative replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "-- harder relative replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "\n",
      "\n",
      "--- working on package: meshAfterParty ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "\n",
      "\n",
      "--- working on package: neuron_morphology_tools ---\n",
      "-- easy initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "-- harder initial replacement --\n",
      "# of substitutions = 0\n",
      "  --> output_filepath = /neurd_packages/graph_tools/graph_tools/null_models.py\n",
      "# of multi-line strings = 0\n",
      "# of matches (unique = True) = 7\n",
      "# of modules replaced = 7\n",
      "----non_pkg_mods_str = \n",
      "from collections import Counter\n",
      "from networkx.generators.classic import empty_graph, path_graph, complete_graph\n",
      "import matplotlib.pyplot as plt\n",
      "import networkx as nx\n",
      "import numpy as np\n",
      "import random\n",
      "import time\n",
      "\n",
      "\n",
      "----pkg_mods_str = \n",
      "\n",
      "\n",
      "\n",
      "----own_mod_str = \n",
      "\n"
     ]
    }
   ],
   "source": [
    "from datasci_tools import package_utils as pku\n",
    "pku.clean_package_syntax(\n",
    "    directory = [\n",
    "        directory,\n",
    "    ],\n",
    "    create_init_if_not_exist = True,\n",
    "    overwrite = True,\n",
    "    verbose = True,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Cleaning all other packages for this name"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "('/neurd_packages/datasci_tools/datasci_tools/',\n",
       " '/neurd_packages/machine_learning_tools/machine_learning_tools/',\n",
       " '/neurd_packages/pytorch_tools/pytorch_tools/',\n",
       " '/neurd_packages/graph_tools/graph_tools/',\n",
       " '/neurd_packages/meshAfterParty/meshAfterParty/',\n",
       " '/neurd_packages/neuron_morphology_tools/neuron_morphology_tools/')"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pku.user_packages"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pku.prefix_module_imports_in_files(\n",
    "    #filepaths = [\"/neurd_packages/meshAfterParty/meshAfterParty/dataInterface.py\"],\n",
    "    modules_directory=directory,\n",
    "    filepaths_directory = pku.user_packages,\n",
    "    overwrite_file = True,\n",
    "    verbose = True,\n",
    "    debug_files = False,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Requirmenets (from in the bash if fail to get error message)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "from datasci_tools import requirement_utils as requ"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      "  0%|          | 0/1 [00:00<?, ?it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "command = pipreqs --encoding=utf8 --force graph_tools --ignore=graph_tools/.ipynb_checkpoints,graph_tools/old_modules,graph_tools/__pycache__ --mode gt --savepath /neurd_packages/graph_tools/requirements.txt\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:02<00:00,  2.09s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Package Diff: ['collections' 'itertools' 'random' 'time']\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "{'graph_tools': {'matplotlib': '3.3.4',\n",
       "  'ndlib': '5.1.1',\n",
       "  'netsci': '0.0.3',\n",
       "  'networkx': '2.5',\n",
       "  'numpy': '1.19.5',\n",
       "  'pandas': '1.1.5',\n",
       "  'powerlaw': '1.5',\n",
       "  'datasci_tools': '0.0.1',\n",
       "  'scipy': '1.5.4',\n",
       "  'seaborn': '0.11.2',\n",
       "  'tqdm': '4.62.2',\n",
       "  'ipython': None,\n",
       "  'ipython_genutils': None}}"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Generate the requirements package\n",
    "from datasci_tools import requirement_utils as requ\n",
    "\n",
    "req_dict = requ.requirements_dict_from_directories(\n",
    "    directories=(directory_name,),\n",
    "    verbose = True,\n",
    ")\n",
    "req_dict"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Do the setup.py"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from datasci_tools import setup_py_utils as setu\n",
    "setu.setup_py_str_generator(\n",
    "    directory_name,\n",
    "    output_path=\"./setup.py\"\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Try to pip install (and manually fix any versions that have conflicts, like with python version)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#!pip3 install -e ."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Create the github documentation (instructions in documentation.txt)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
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  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
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